3LTN

Inhibitor-stabilized topoisomerase IV-DNA cleavage complex (S. pneumoniae)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 

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This is version 1.2 of the entry. See complete history


Literature

Structural Basis of Gate-DNA Breakage and Resealing by Type II Topoisomerases

Laponogov, I.Pan, X.-S.Veselkov, D.A.McAuley, K.E.Fisher, L.M.Sanderson, M.R.

(2010) PLoS One 5: e11338-e11338

  • DOI: https://doi.org/10.1371/journal.pone.0011338
  • Primary Citation of Related Structures:  
    3K9F, 3KSA, 3KSB, 3LTN

  • PubMed Abstract: 

    Type II DNA topoisomerases are ubiquitous enzymes with essential functions in DNA replication, recombination and transcription. They change DNA topology by forming a transient covalent cleavage complex with a gate-DNA duplex that allows transport of a second duplex though the gate. Despite its biological importance and targeting by anticancer and antibacterial drugs, cleavage complex formation and reversal is not understood for any type II enzyme. To address the mechanism, we have used X-ray crystallography to study sequential states in the formation and reversal of a DNA cleavage complex by topoisomerase IV from Streptococcus pneumoniae, the bacterial type II enzyme involved in chromosome segregation. A high resolution structure of the complex captured by a novel antibacterial dione reveals two drug molecules intercalated at a cleaved B-form DNA gate and anchored by drug-specific protein contacts. Dione release generated drug-free cleaved and resealed DNA complexes in which the DNA gate instead adopts an unusual A/B-form helical conformation with a Mg(2+) ion repositioned to coordinate each scissile phosphodiester group and promote reversible cleavage by active-site tyrosines. These structures, the first for putative reaction intermediates of a type II topoisomerase, suggest how a type II enzyme reseals DNA during its normal reaction cycle and illuminate aspects of drug arrest important for the development of new topoisomerase-targeting therapeutics.


  • Organizational Affiliation

    Randall Division of Cell and Molecular Biophysics, King's College London, London, United Kingdom.


Macromolecules

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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit A
A, B
496Streptococcus pneumoniaeMutation(s): 0 
Gene Names: ParC
EC: 5.99.1
UniProt
Find proteins for P72525 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore P72525 
Go to UniProtKB:  P72525
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP72525
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
DNA topoisomerase 4 subunit B
C, D
268Streptococcus pneumoniaeMutation(s): 0 
Gene Names: ParE
EC: 5.99.1
UniProt
Find proteins for Q59961 (Streptococcus pneumoniae serotype 4 (strain ATCC BAA-334 / TIGR4))
Explore Q59961 
Go to UniProtKB:  Q59961
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UniProt GroupQ59961
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  • Reference Sequence

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Entity ID: 3
MoleculeChains LengthOrganismImage
5'-D(*AP*CP*CP*AP*AP*GP*GP*T*CP*AP*TP*GP*AP*AP*T)-3'15N/A
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Entity ID: 4
MoleculeChains LengthOrganismImage
5'-D(P*AP*GP*TP*CP*AP*TP*TP*CP*AP*TP*GP*AP*CP*CP*TP*TP*GP*GP*T)-3'19N/A
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Entity ID: 5
MoleculeChains LengthOrganismImage
5'-D(*CP*TP*GP*TP*TP*TP*TP*A*CP*GP*TP*GP*CP*AP*T)-3'15N/A
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Entity ID: 6
MoleculeChains LengthOrganismImage
5'-D(P*GP*AP*CP*TP*AP*TP*GP*CP*AP*CP*GP*TP*AP*AP*AP*AP*CP*AP*G)-3'19N/A
Sequence Annotations
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  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.10 Å
  • R-Value Free: 0.228 
  • R-Value Work: 0.186 
  • R-Value Observed: 0.190 
  • Space Group: P 32
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 122.507α = 90
b = 122.507β = 90
c = 178.303γ = 120
Software Package:
Software NamePurpose
PHASERphasing
PHENIXrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-05-05
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description